Chromosome-length genome assemblies of six legume species provide insights into genome organization, evolution, and agronomic traits for crop improvement

Garg, Vanika; Dudchenko, Olga; Wang, Jinpeng; Khan, Aamir W.; Gupta, Saurabh; Kaur, Parwinder; Han, Kai; Saxena, Rachit K.; Kale, Sandip M.; Pham, Melanie; Yu, Jigao; Chitikineni, Annapurna; Zhang, Zhikang; Fan, Guangyi; Lui, Christopher; Valluri, Vinodkumar; Meng, Fanbo; Bhandari, Aditi; Liu, Xiaochuan; Yang, Tao; Chen, Hua; Valliyodan, Babu; Roorkiwal, Manish; Shi, Chengcheng; Yang, Hong; Durand, Neva C.; Pandey, Manish K.; Li, Guowei; Barmukh, Rutwik; Wang, Xingjun; Chen, Xiaoping; Lam, Hon‐Ming; Jiang, Huifang; Zong, Xuxiao; Liang, Xuanqiang; Liu, Xin; Liao, Boshou; Guo, Bao‐Zhu; Jackson, Scott A.; Nguyen, Henry T.; Zhuang, Weijian; Wan, Shungang; Wang, Xiyin; Aiden, E; Bennetzen, Jeffrey L.; Varshney, Rajeev K.

doi:10.1016/j.jare.2021.10.009

Cited by 28 publications

(26 citation statements)

References 86 publications

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“…Wide variability, insensitivity to G × E interaction, and high heritability of Ca identify this nutrient to have stable trait-associated variants in genome-wide association studies (GWAS). The availability of reference genome sequence in pigeonpea ( Varshney et al, 2012 ; Garg et al, 2021 ) facilitates the application of GWAS to understand the genetic basis of grain nutrient accumulation and to identify candidate genes or genomic regions associated with these nutrients in future studies to breed biofortified pigeonpea cultivars. However, earlier studies pertaining to the association of genomic regions with domestication and agronomic traits were reported ( Varshney et al, 2017 ; Zhao et al, 2020 ).…”

Section: Discussionmentioning

confidence: 99%

Grain Nutrients Variability in Pigeonpea Genebank Collection and Its Potential for Promoting Nutritional Security in Dryland Ecologies

et al. 2022

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Pigeonpea, a climate-resilient legume, is nutritionally rich and of great value in Asia, Africa, and Caribbean regions to alleviate malnutrition. Assessing the grain nutrient variability in genebank collections can identify potential sources for biofortification. This study aimed to assess the genetic variability for grain nutrients in a set of 600 pigeonpea germplasms conserved at the RS Paroda Genebank, ICRISAT, India. The field trials conducted during the 2019 and 2020 rainy seasons in augmented design with four checks revealed significant differences among genotypes for all the agronomic traits and grain nutrients studied. The germplasm had a wider variation for agronomic traits like days to 50% flowering (67–166 days), days to maturity (112–213 days), 100-seed weight (1.69–22.17 g), and grain yield per plant (16.54–57.93 g). A good variability was observed for grain nutrients, namely, protein (23.35–29.50%), P (0.36–0.50%), K (1.43–1.63%), Ca (1,042.36–2,099.76 mg/kg), Mg (1,311.01–1,865.65 mg/kg), Fe (29.23–40.98 mg/kg), Zn (24.14–35.68 mg/kg), Mn (8.56–14.01 mg/kg), and Cu (7.72–14.20 mg/kg). The germplasm from the Asian region varied widely for grain nutrients, and the ones from African region had high nutrient density. The significant genotype × environment interaction for most of the grain nutrients (except for P, K, and Ca) indicated the sensitivity of nutrient accumulation to the environment. Days to 50% flowering and days to maturity had significant negative correlation with most of the grain nutrients, while grain yield per plant had significant positive correlation with protein and magnesium, which can benefit simultaneous improvement of agronomic traits with grain nutrients. Clustering of germplasms based on Ward.D2 clustering algorithm revealed the co-clustering of germplasm from different regions. The identified top 10 nutrient-specific and 15 multi-nutrient dense landraces can serve as promising sources for the development of biofortified lines in a superior agronomic background with a broad genetic base to fit the drylands. Furthermore, the large phenotypic data generated in this study can serve as a raw material for conducting SNP/haplotype-based GWAS to identify genetic variants that can accelerate genetic gains in grain nutrient improvement.

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Section: Discussionmentioning

confidence: 99%

Grain Nutrients Variability in Pigeonpea Genebank Collection and Its Potential for Promoting Nutritional Security in Dryland Ecologies

et al. 2022

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“…Furthermore, the A02487 (Q9UWF0) and A03535 (I1RNF9) genes in A. rasikravindrae were paired with the CAM gene of M. oryzae, which caused rice blast and head blast in host Triticum aestivum [76], and the GzGPA1 gene of Fusarium graminearum, which caused Improved genome assembly and exact gene collinearity ensure the inference of thousands of plausible homologs arising from evolutionary events, polyploidization, or speciation. Collinear homologs were likely to be generated simultaneously in corresponding events [43]. Our results showed 11,040 collinearity blocks in A. rasikravindrae and A. phaeospermum which resembled 73.99% of the entire gene length (48,449,939 bp), thus representing a large linear correlation between both fungal species.…”

Section: Discussionmentioning

confidence: 58%

“…Improved genome assembly and exact gene collinearity ensure the inference of thousands of plausible homologs arising from evolutionary events, polyploidization, or speciation. Collinear homologs were likely to be generated simultaneously in corresponding events [ 43 ]. Our results showed 11,040 collinearity blocks in A. rasikravindrae and A. phaeospermum which resembled 73.99% of the entire gene length (48,449,939 bp), thus representing a large linear correlation between both fungal species.…”

Section: Discussionmentioning

confidence: 99%

“…Previous studies have reported that various organisms have been utilized for genomic transformations as individuals or cells, such as the Cancer Genome Association and Arabidopsis Genome Project [ 42 ]. Significant efforts have been made in the past five years to improve assemblies of genomes, and the improvement of nearly complete genomes using long-read sequencing technologies [ 43 ]. Simultaneously, there are no whole genomic studies have been found of A. rasikravindrae worldwide.…”

Section: Introductionmentioning

confidence: 99%

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The First Whole Genome Sequence Discovery of the Devastating Fungus Arthrinium rasikravindrae

Majeedano

Chen

Zhu

et al. 2022

JoF

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Devastating fungi are one of the most important biotic factors associated with numerous infectious diseases not only in plants but in animals and humans too. Arthrinium rasikravindrae a devastating fungus is responsible for severe infections in a large number of host plants all over the world. In the present study, we analyzed the whole genome sequence of devastating fungus A. rasikravindrae strain AQZ-20, using Illumina Technology from the Novogene Bio-informatics Co., Ltd. Beijing, China. To identify associated annotation results, various corresponding functional annotations databases were utilized. The genome size was 48.24 MB with an N90 (scaffolds) length of 2,184,859 bp and encoded putative genes were 11,101, respectively. In addition, we evaluated the comparative genomic analyses with 4 fungal strains of Ascomycetes. Two related species showed a strong correlation while others exhibited a weak correlation with the A. rasikravindrae AQZ-20 fungus. This study is a discovery of the genome-scale assembly, as well as annotation for A. rasikravindrae. The results obtained from the whole genome sequencing and genomic resources developed in this study will contribute significantly to genetic improvement applications against diseases caused by A. rasikravindrae. In addition, the phylogenetic tree, followed by genomic RNA, transcriptomic, proteomic, metabolic, as well as pathogenic data reported in current research will provide deep insight for further studies in the future.

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“…A:T > G:C and C:G > T:A transitions can be introduced directly into targeted sites by using adenosine deaminase (adenine base editor, ABE) and cytidine deaminase (cytosine base editor, CBE), respectively ( Zhu et al, 2020 ). Next-generation sequencing technologies have led to the development of genome assemblies for a number of legume crops even if they are fragmented ( Garg et al, 2021 ). These genomic information are used to modify key regions of genes in order to increase yield and quality, as well as other agronomic traits.…”

Section: Gene-editing Technologiesmentioning

confidence: 99%

Gene-Editing Technologies and Applications in Legumes: Progress, Evolution, and Future Prospects

et al. 2022

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Legumes are rich in protein and phytochemicals and have provided a healthy diet for human beings for thousands of years. In recognition of the important role they play in human nutrition and agricultural production, the researchers have made great efforts to gain new genetic traits in legumes such as yield, stress tolerance, and nutritional quality. In recent years, the significant increase in genomic resources for legume plants has prepared the groundwork for applying cutting-edge breeding technologies, such as transgenic technologies, genome editing, and genomic selection for crop improvement. In addition to the different genome editing technologies including the CRISPR/Cas9-based genome editing system, this review article discusses the recent advances in plant-specific gene-editing methods, as well as problems and potential benefits associated with the improvement of legume crops with important agronomic properties. The genome editing technologies have been effectively used in different legume plants including model legumes like alfalfa and lotus, as well as crops like soybean, cowpea, and chickpea. We also discussed gene-editing methods used in legumes and the improvements of agronomic traits in model and recalcitrant legumes. Despite the immense opportunities genome editing can offer to the breeding of legumes, governmental regulatory restrictions present a major concern. In this context, the comparison of the regulatory framework of genome editing strategies in the European Union and the United States of America was also discussed. Gene-editing technologies have opened up new possibilities for the improvement of significant agronomic traits in legume breeding.

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Chromosome-length genome assemblies of six legume species provide insights into genome organization, evolution, and agronomic traits for crop improvement

Cited by 28 publications

References 86 publications

Grain Nutrients Variability in Pigeonpea Genebank Collection and Its Potential for Promoting Nutritional Security in Dryland Ecologies

Grain Nutrients Variability in Pigeonpea Genebank Collection and Its Potential for Promoting Nutritional Security in Dryland Ecologies

The First Whole Genome Sequence Discovery of the Devastating Fungus Arthrinium rasikravindrae

Gene-Editing Technologies and Applications in Legumes: Progress, Evolution, and Future Prospects

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